Communicating the subtle motion of molecular systems over time can be a challenge. Whether you’re refining a drug candidate through conformational sampling or analyzing a simulation trajectory frame by frame, one of the key difficulties for molecular modelers is presenting dynamic behavior in a way that’s both smooth and informative.
This is where SAMSON’s Play path animation can make a real difference. This feature helps you visualize and present molecular movements between keyframes using stored trajectory paths—perfect for comparing conformations or cycling through results from simulations.
What is a Path?
In SAMSON, a path node stores a trajectory made of successive molecular conformations. This might result from a molecular dynamics simulation, energy landscape exploration, or any other motion-based modeling task. These paths contain frames, and each frame represents a conformation of the molecular model.
Why Use the Play Path Animation?
If you’ve ever wanted to animate a structure transitioning through conformations—for example in a trajectory output from a simulation—the Play path animation simplifies this process by syncing the trajectory frames with animation frames inside SAMSON’s Animator. It allows seamless playback without the need to manually match up intricate frame sequences.
Some key uses include:
- Playing through conformations of a ligand binding process
- Animating protein folding transitions captured in a path
- Looping a conformational search to analyze changes
How to Add a Play Path Animation
1. First, choose the path node you want to visualize.
2. Open the Animation panel of the Animator.
3. Double-click on the Play path animation effect.
4. Two keyframes will be added automatically—these define the start and end of the animation.
5. Move or adjust these keyframes as needed to control speed and timing.
Smoothing and Synchronization
By default, the animation applies smoothing to ensure fluid motion, which is especially useful if the number of path frames and animation frames differ. However, if you want each frame to correspond exactly without interpolation—for example, when highlighting specific intermediate states—you can disable smoothing in the Inspector.
Moreover, if you apply the animation to multiple paths at once, the transitions will be synchronized. This feature is helpful when comparing multiple simulations side by side (e.g., comparing a wild-type vs mutant conformation change).
Customizing the Look and Feel
Don’t forget you can adjust the easing curve to change the rate of interpolation across your animation frames. This helps you tailor the playback for clarity, acceleration effects, or dramatic emphasis depending on your presentation needs.
A Better Way to Communicate Motion
Animations are not just visual flourishes. For molecular modelers, being able to clearly and accurately communicate time-dependent behaviors is essential—whether it’s reporting to collaborators, teaching, or understanding mechanistic pathways. The Play path animation offers a clear and intuitive way to bring static trajectories to life.
To learn more, see the full documentation at
https://documentation.samson-connect.net/users/latest/animations/play-path/
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON and explore SAMSON Extensions at https://www.samson-connect.net.